Debugging first step.

Docker/Dockerfile-vlbi

@@ -3,5 +3,12 @@ FROM lofareosc/prefactor3-cwl
 RUN python3 -m pip install -Iv pyvo==0.9.3
 RUN apt-get update && \
     apt-get install -y git
-RUN git clone https://github.com/lonbar/VLBI-cwl.git /root/VLBI-cwl
-ENV PYTHONPATH=/root/VLBI-cwl/scripts/:$PYTHONPATH
+
+RUN groupadd -r lofaruser && \
+    useradd -r -l -m -g lofaruser lofaruser
+
+WORKDIR /home/lofaruser
+
+USER lofaruser
+RUN git clone https://github.com/lonbar/VLBI-cwl.git /home/lofaruser/VLBI-cwl
+ENV PYTHONPATH=/home/lofaruser/VLBI-cwl/scripts/:$PYTHONPATH

scripts/compareStationListVLBI.py

@@ -28,7 +28,8 @@ def plugin_main(args, **kwargs):
     filter         = kwargs['filter']
     #data           = DataMap.load(mapfile_in)
     #mslist         = [data[i].file for i in xrange(len(data))]
-    mslist         = args['mss']
+    mslist         = args #['mss']
+    print(mslist)
 
     if len(mslist) == 0:
         raise ValueError("Did not find any existing directory in input MS list!")

steps/check_station_mismatch.cwl

@@ -33,7 +33,9 @@ requirements:
           entry: |
             import sys
             import json
-            from compareStationListVLBI import main as compareStationList
+            import os
+            print(os.environ)
+            from compareStationListVLBI import plugin_main as compareStationList
 
             mss = sys.argv[1:]
             inputs = json.loads(r"""$(inputs)""")
@@ -42,7 +44,7 @@ requirements:
             filter = inputs['filter_baselines']
             print(mss)
 
-            output = compareStationList(mss = mss, 
+            output = compareStationList(mss, 
                                         h5parmdb = h5parmdb, 
                                         solset_name = solset_name, 
                                         filter = filter)
@@ -69,7 +71,7 @@ outputs:
 
 hints:
   DockerRequirement:
-    dockerPull: vlbi-cwl
+    dockerPull: vlbi-cwl:latest
 
 stdout: compareStationMismatch.log
 stderr: compareStationMismatch_err.log

test.json

 {
-  "msin": {
-    "class": "Directory",
-    "path": [
-      "/home/tjlv53/test_data/L693719_SB000_uv.MS"
-    ]
-  },
-  "solset": [
-    {
-      "class": "File",
-      "path": "/home/tjlv54/test_data/P205+55/Pre-Facet-Calibrator/results/cal_values/cal_solutions.h5"
-    }
-  ]
+    "msin": [
+                {"class": "Directory", "path": "/home/tjlv53/software/VLBI-cwl/test_data/L693719_SB000_uv.MS"}
+            ],
+    "solset": {"class": "File", "path": "/home/tjlv53/software/VLBI-cwl/test_data/P205+55:Pre-Facet-Calibrator/results/cal_values/cal_solutions.h5"}
 }